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Jacob Arie van Diermen
MSc
Profile
Personal profile
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I am an enthusiastic aspiring researcher that is passionate about solving complex biological questions. To pursue this goal, I want to use new computational tools and large-scale omics techniques. Currently developed omics techniques allows us to answer exciting biological questions that were out of reach not too long ago. Furthermore, I aspire to further develop my skills in analyzing, visualizing and interpreting these large omics datasets, which is helped by my extensive biological background.
Education
Utrecht university, Graduate School of Life Sciences
MSc Molecular and Cellular life sciences (MCLS), specialization Biophysics & Molecular Imaging, Bioinformatics minor profile
Utrecht, The Netherlands
2023 - 2020
Final grade: 8.02/10
Bioinformatics minor profile
- Thesis: Comparative genomics approach finds DNA-repair and immune-related genes in the regenerative African spiny mouse
Major research project
- Thesis: Characterization of CSPP1 interaction with microtubules in cells
Utrecht university, Department of Biology
BSc in Biology
Utrecht, The Netherlands
2020 - 2017
graduated with honors (cum laude)
Final grade: 8.14/10
Bachelor thesis: Promising molecular targets for therapeutic intervention in Alzheimer’s disease
Research Experience
Research assistant
Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)
Solna, Sweden
2024/03 - 2023/07
- Creating Docker and Singularity containers for the positive selection pipeline
- Working with positive selection tools like HyPhy MEME. HyPhy aBSREL and PAML codeml
- Experience working with the Linux operating system (Ubuntu, Pop!_OS)
- Writing paralleled bash and R scripts for the positive selection pipeline
- Accessing and working with publicly available single-cell datasets from GTEX
- Preparing and writing a manuscript for publication
- Presenting data at lab meetings
- Preparing and writing a manuscript for publication
- Continuation of the research project as a research assistant
Teaching assistant
Utrecht university, Department of Biology
Utrecht, The Netherlands
2023/05 - 2023/02
Teaching assistant for the course Kwantitatieve biologie (B-B1KWBI20),
a quantitative biology course for first year biology students.
Research intern
Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)
Solna, Sweden
2023/03 - 2022/05
- Construction of a custom positive selection analysis pipeline for a large number of multiple sequence alignments
- Working with positive selection tools like HyPhy MEME, HyPhy aBSREL and PAML codeml
- Experience with High performance computing in a SLURM environment
- Adept programming experience in R, Python and bash
- Experience with Git and github
- Working with genomics data
- Gene ontology analyses
- Cytoscape and STRINGdb network analysis
- Creation of data visualizations using R
- Presenting and writing skills
- Creation of a scientific poster for a conference
Research intern
Utrecht university, Cell biology, neurobiology and biophysics, Anna Akhmanova Group (Cellular dynamics)
Utrecht, The Netherlands
2022/03 - 2021/01
- Extensive cell culture with mammalian adherent cell lines (COS7, RPE, HeLa)
- Molecular cloning with SNAPtag, LEXY, PA-GFP, EB3 constructs
- Transfections
- Transformation of E.coli
- Western blots (Semi-dry blotting)
- PCR
- Immunofluorescence staining
- Fluorescence microscopy
- Expansion microscopy (STED)
- Live-cell imaging (spinning disk, TIRF)
- Experiment planning
- Presenting data
- General lab skills
Additional skills
Software skills
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- Docker
- Singularity
- Git
- Github
- Rsudio
- R
- Python
- Bash
- Anaconda
- HyPhy (aBSREL, MEME)
- PAML codeml
- GraphPad Prism 8
- Fiji/ ImageJ
- Biorender
- Cytoscape
Talks and conferences
Genetic deconvolution of regenerative phenotypes in Acomys cahirinus
Tissue and Motion Conference 2022 (Poster)
Djurhamn, Sweden
2022
Jacob A. van Diermen, Sebastian A. Lewandowski, Katarina Tengvall, Michael Dong, Kerstin Lindblad-Toh
Recognition
Theme winner (Energy) Sustainable campus challenge 2020
Utrecht Challenge Alliance
Utrecht, The Netherlands
2020
I participated in the sustainable campus challenge 2020 organized by the Utrecht challenge alliance. This is a partnership for open innovation to find regional solutions to social issues in cooperation between companies, public organisations, governments and educational institutions. We were tasked to come up with a concept to reduce the energy usage of student housing and came up with a concept that rewards students for their sustainable behaviour. Our concept was chosen as the best concept to reduce student energy usage.
Latin honors (Cum laude) for BSc in Biology
Utrecht university, Department of Biology
Utrecht, The Netherlands
2020
MSc Molecular and Cellular life sciences (MCLS) courses
Minor Research Project (GSLS-MINRP)
Comparative genomics approach finds DNA-repair and immune-related genes in the regenerative African spiny mouse
Solna, Sweden
2023/03 - 2022/05
8.6/10
Major Research Project (GSLS-MAJRP)
Major Research Project Characterization of CSPP1 interaction with microtubules in cells
Utrecht, The Netherlands
2022/03 - 2021/01
7.5/10
Writing Assignment (Literature Review) (GSLS-WRIAS)
DNA methylation signals in blood as proxies for environmental exposures
Utrecht, The Netherlands
2023
7.3/10
Advanced R for Life Sciences: In-depth Techniques for analysis, visualization and publishing (B-MADR19)
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N/A
2022
9.7/10
Advanced Omics for Life Sciences (BMB502316)
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N/A
2022
8.5/10
Basic Machine Learning for Bioinformatics (B-MBIOBMLB)
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N/A
2022
8.1/10
Introduction to Bioinformatics for Life Sciences (B-MINBI19)
N/A
N/A
2021
8.6/10
Advanced Microscopy (NS-EX423M)
N/A
N/A
2021
7.9/10
Applied Cryo-Electron Microscopy (SK-MCACEM)
N/A
N/A
2021
8.1/10
Master Course Molecules & Cells (SK-MCMC)
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2020
7.4/10
Master Course Biophysics & Molecular Imaging (SK-MCBMI)
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N/A
2020
8.6/10
BSc in Biology courses
bachelor thesis Cell biology (B-B3ONSCR)
Promising molecular targets for therapeutic intervention in Alzheimer’s disease
Utrecht, The Netherlands
2020
8.5/10
Research internship cell biology (B-B3ONST)
Modulation of GABAergic transmission via GABA shift timing
Utrecht, The Netherlands
2020
8.0/10
Voortgezette statistiek en ‘R’ (B-B2VSR)
Advanced statistics and ‘R’
N/A
2020
7.4/10
Licht en electronen microscopie (B-B3LEM18)
Light and electron microscopy
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2020
7.9/10
Molecular cell research (B-B3MCR18)
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2020
7.9/10
Neuronale aandoeningen (B-B3NAAN16)
Neuronal disorders
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2020
8.1/10
Biologische modellering (B-B2THEC05)
Biological modelling
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2019
8.3/10
Cellen en weefsels (B-B3CEWE)
Cells and tissues
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2019
8.0/10
Immunobiologie (B-B3IMMB09)
Immunobiology
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2019
8.6/10
Moleculaire eukaryote microbiologie (B-B3EUKA09)
Molecular eukaryotic microbiology
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2019
9.7/10
De Cel (B-B2CEL09)
The cell
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2019
8.8/10
Data science en biologie (B-B2DSB18)
Data science and biology
N/A
2019
8.1/10
Moleculair genetische onderzoekstechniek (B-B2MGOT14)
Molecular and genetic research techniques
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2019
7.0/10
Ontwikkelingsbiologie (B-B2OBI07)
Developmental biology
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2018
8.0/10
Metabolisme (B-B2META09)
Metabolism
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2018
8.1/10
Neurobiologie (B-B2NEUR10)
Neurobiology
N/A
2018
8.5/10
Biotechnologie en maatschappij (B-B1BIOT09)
Biotechnology and society
N/A
2018
8.4/10
Academisch schrijven (B-B2AS17)
Academical writing
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2018
7.6/10
Experiment en statistiek (B-B1EXST13)
Experiments and statistics
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2018
8.2/10
Systeembiologie (B-B1SYSB09)
Systems biology
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2018
9.0/10
Biologie en ecologie van planten (B-B1BEP13)
Biology and ecology of plants
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2018
7.8/10
Biologie van dieren (B-B1DIER05)
Biology of animals
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2018
7.3/10
Evolutie en biodiversiteit (B-B1EVBI13)
Evolution and biodiversity
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2017
7.8/10
Moleculaire biologie (B-B1MB05)
Molecular biology
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2017
8.3/10